7.6. MedEx-UIMA drug NLP¶
MedEx-UIMA NLP (for drugs and drug doses) [1] is supported via an external program. MedEx-UIMA runs in Java. CRATE supplies an external front-end Java program (CrateMedexPipeline.java) that loads the MedEx app, sends text to it (via a temporary disk file, for reasons relating to MedEx-UIMA’s internal workings), and returns answers.
7.6.1. Installation¶
- Download it from https://sbmi.uth.edu/ccb/resources/medex.htm
- CRATE provides Java code (see CrateMedexPipeline.java) to talk to
MedEx-UIMA. Use
crate_nlp_build_medex_java_interface
to build this before you use it for the first time. - CRATE fixes some bugs in MedEx-UIMA. Run
crate_nlp_build_medex_itself
to rebuild MedEx and fix them.
7.6.2. crate_nlp_build_medex_java_interface¶
Options as of 2017-02-28:
usage: crate_nlp_build_medex_java_interface [-h] [--builddir BUILDDIR]
[--medexdir MEDEXDIR]
[--java JAVA] [--javac JAVAC]
[--verbose] [--launch]
Compile Java classes for CRATE's interface to MedEx-UIMA
optional arguments:
-h, --help show this help message and exit
--builddir BUILDDIR Output directory for compiled .class files (default: /h
ome/rudolf/Documents/code/crate/crate_anon/nlp_manager/
compiled_nlp_classes)
--medexdir MEDEXDIR Root directory of MedEx installation (default:
/home/rudolf/dev/Medex_UIMA_1.3.6)
--java JAVA Java executable (default: java)
--javac JAVAC Java compiler (default: javac)
--verbose, -v Be verbose (use twice for extra verbosity)
--launch Launch script in demonstration mode (having previously
compiled it)
7.6.3. crate_nlp_build_medex_itself¶
This program builds MedEx and implements some bug fixes and improvements for the UK.
Options as of 2017-02-28:
usage: crate_nlp_build_medex_itself [-h] [--medexdir MEDEXDIR] [--javac JAVAC]
[--deletefirst] [--verbose]
Compile MedEx-UIMA itself (in Java)
optional arguments:
-h, --help show this help message and exit
--medexdir MEDEXDIR Root directory of MedEx installation (default:
/home/rudolf/dev/Medex_UIMA_1.3.6)
--javac JAVAC Java compiler (default: javac)
--deletefirst Delete existing .class files first (optional)
--verbose, -v Be verbose
Footnotes
[1] | MedEx UIMA reference publication: https://www.ncbi.nlm.nih.gov/pubmed/25954575 |
[2] | MedEx-UIMA downloads: https://sbmi.uth.edu/ccb/resources/medex.htm |